1. The particular lease terms will determine how you are paid, when, and for what. However, most leases being taken today, particularly in the Tuscaloosa Marine Shale, are "paid-up" leases, meaning you receive a one-time bonus payment rather than a periodic rental payment. Based on what you posted, and "common practice," it appears you are being offered a $100 per acre, one-time signing bonus for granting a three year lease. The bonus would normally be paid in full at the time you sign the lease.
2. Operators rarely, if ever, lease the surface land itself. A standard oil and gas lease in Louisiana gives the company the right to use land for the well location, but only so much as is "reasonably necessary." Simply put, even though the well will be horizontal, they have to poke a hole somewhere. Typically well locations will not be on tracts smaller than 20 acres, and there are laws regulating how many feet away from a building a well can be. If you are concerned about your surface land being used for drilling or operations, you could request that your lease have a "no surface operations" clause that prohibits such activity. If your tract is small, this should not be a problem for the lessee.